nf-core/plink/indeppairwise @ 0.0.0-0c7146d
Summary
Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain.
Get started
Add the following snippet to your workflow script to include this module.
include { PLINK_INDEPPAIRWISE } from 'nf-core/plink/indeppairwise'
License
MIT License
Name
|
PLINK_INDEPPAIRWISE |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bed
file
|
PLINK binary biallelic genotype table file *.{bed}
|
bim
file
|
PLINK extended MAP file *.{bim}
|
fam
file
|
PLINK sample information file *.{fam}
|
window_size
string
|
Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. |
|---|
variant_count
string
|
Variant count to shift the window at the end of each step. |
|---|
r2_threshold
string
|
Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain |
|---|
prunein
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.prune.in
file
|
File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other *.{prune.in}
|
pruneout
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.prune.out
file
|
File with IDs of excluded variants *.{prune.out}
|
versions_plink
tuple
${task.process}
string
|
The name of the process |
|---|---|
plink
string
|
The name of the tool |
plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| plink | Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | https://www.cog-genomics.org/plink |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:04:19 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplink%2Findeppairwise/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plink/indeppairwise/blobs/sha256:8707fca9eeef7aaea965ae2d7b54b8f603f8d5da7fe5c3fa8a64b362f52c2897 |
| Size | 3.0 KB |
| Checksum | sha256:8707fca9eeef7aaea965ae2d7b54b8f603f8d5da7fe5c3fa8a64b362f52c2897 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:04:19 (UTC) | 1 | 3.0 KB | - |